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phyloXML : XML for evolutionary biology and comparative genomics

PhyloXML is an XML language designed to contain detailed information about evolutionary trees and related data. It aims to address the lack of standardized methods for annotating tree nodes and branches with unique attributes. PhyloXML supports various software tools for reading, writing, and visualizing phylogenetic data, such as BioPerl, BioRuby, and Biopython. These tools facilitate conversions from existing formats and help integrate diverse data types into a single tree structure, enhancing the storage and retrieval of biological datasets.

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phyloXML : XML for evolutionary biology and comparative genomics

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  1. phyloXML: XML for evolutionary biology and comparative genomics Han, Mira and Zmasek, Christian

  2. Biology Com.Sci Database Biological database NCBI,Uniprot… Server Applications Application Bioperl, BioRuby, BioPhyton Visual Representaion In browser Visual Representaion In browser TreeJuxtaposer, TreeJview….

  3. Present & future • the lack of standardized means to annotate tree nodes and branches with distinct attributes. • Current formats - Nexus or NHX (New Hampshire eXtended) • Previous proposals for a XML format for systematic data never gained popularity, possibly due to a lack of supporting software.

  4. PyloXML • PhyloXMLis an XML language defined by a complete schema in XSD , for describing evolutionary trees, as well as various associated data items • various software tools for reading, writing, conversion, and visualization of phyloXML formatted data.

  5. Tools • The Java command-line "phyloxml_converter" can convert existing into phyloXML. • “Decorator" helps the users insert various data types into a phyloXML tree. • phyloXML support has been developed for three open source namely • BioPerl (module Bio::TreeIO::phyloxml) • BioRuby(module Bio::PhyloXML) • Biopython(module Bio.Tree.PhyloXML)  

  6. My inference • Data structure is vital for efficient information retrieval ,updating and processing • As biology dataset are huge less explored , these formats will improve the weak link. • So Data structure in XML format is like tree structure so the algorithm for the basic process could be log h.

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